At Oxford, he became successively student and tutor of Christ Church. In 1811, he was appointed Regius Professor of Greek in the University. Taking orders, he held (1815–1847) the college living of Westwell, Oxfordshire, and other ecclesiastical preferments simultaneously with his professorship. In 1829, he was offered the position of Bishop of Oxford, but he turned it down. From 1831 until his death, he was Dean of Christ Church.

On 11 May 1815 Gaisford married Helen Margaret Douglas the daughter of the Rev. Robert Douglas. They had five children. After she died in 1830, he married Jane Catharine Jenkyns (1787–1863); she was the sister of Dr Richard Jenkyns, master of Balliol College and Dr Henry Jenkyns.

On 23 June 1843, Gaisford's 21 year-old son, William Gaisford, drowned while swimming in the river Thames at Sandford Lock - a notoriously dangerous spot. He got into difficulties and his friend, Richard Phillimore (the son of Joseph Phillimore), entered the water to save him. However, both men perished. They are buried in Christ Church Cathedral. They are commemorated by an obelisk at Sandford Lock and two memorial tablets in the north walk of the Cathedral cloisters.[1]

"Nor can I do better, in conclusion, than impress upon you the study of Greek literature, which not only elevates above the vulgar herd, but leads not infrequently to positions of considerable emolument." –Th. Gaisford, Christmas Day Sermon in the Cathedral, Oxford (Rev. W. Tuckwell, Reminiscences of Oxford, 2nd ed., 1907, p. 124)